Installation#
Requirements#
Biotite requires a modern Python installation (at least the last two years are supported) and the following packages:
numpy
requests
msgpack
networkx
Installation of the biotite
package will also automatically install these
dependencies if not already present.
Some functionalities require extra packages:
matplotlib
- Required for plotting purposes.
Installation from PyPI#
Biotite is available as wheels for a variety of platforms (Windows, Linux, OS X). Simply type
$ pip install biotite
If pip finds an appropriate wheel for your system configuration on PyPI, it will download and install it. If no fitting wheel is found, pip will fall back to the source distribution. In this case, installation will take longer, because extension modules need to be compiled first. Note that this requires a C-compiler (typically GCC) installed on your system.
Installation via Conda#
Biotite is also available via Conda.
$ conda install -c conda-forge biotite
Installation from source#
You can also install Biotite from the
project repository.
However, in addition to building and installing the package, the internal
Chemical Component Dictionary (CCD). for
biotite.structure.info
needs to be built with the setup_ccd
module.
The script in turn requires Biotite.
The solution to this chicken-and-egg problem is to first install Biotite without the
CCD and build the CCD afterwards.
After cloning the repository, navigate to its top-level directory (the one
setup.py
is in) and type the following:
$ pip install .
$ python -m biotite.setup_ccd
setup_ccd.py
can also be used to update the internal CCD to the current upstream
version from the PDB.
Having the Biotite installation always pointing to your repository clone is also possible. Substitute the installation with the following commands instead:
$ pip install -e .
$ python -m biotite.setup_ccd
Common issues and solutions#
Compiler error when building Biotite#
There is a known problem with GCC compiler errors in some Linux distributions (e.g. Arch Linux) when building Biotite from source. Among other error lines the central error is the following:
unable to initialize decompress status for section .debug_info
While the exact reason for this error is still unknown, this can be fixed by using a GCC installed via Conda:
$ conda install -c conda-forge c-compiler
ValueError when importing Biotite#
When importing one of Biotite’s subpackages one of the following errors might occur:
ValueError: numpy.ufunc size changed, may indicate binary incompatibility.
ValueError: numpy.ndarray size changed, may indicate binary incompatibility.
The reason for this error is, that Biotite was built against a NumPy version other than the one installed. This happens for example when NumPy is updated, but Biotite is already installed. Try updating NumPy and Biotite to solve this issue.